Converting Energy Parameter Files

Converting energy parameter files into the latest format.

To preserve some backward compatibility the RNAlib also provides functions to convert energy parameter files from the format used in version 1.4-1.8 into the new format used since version 2.0

Defines

VRNA_CONVERT_OUTPUT_ALL: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of a complete parameter set

VRNA_CONVERT_OUTPUT_HP: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of hairpin contributions

VRNA_CONVERT_OUTPUT_STACK: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of base pair stack contributions

VRNA_CONVERT_OUTPUT_MM_HP: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of hairpin mismatch contribution

VRNA_CONVERT_OUTPUT_MM_INT: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of interior loop mismatch contribution

VRNA_CONVERT_OUTPUT_MM_INT_1N: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 1:n interior loop mismatch contribution

VRNA_CONVERT_OUTPUT_MM_INT_23: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 2:3 interior loop mismatch contribution

VRNA_CONVERT_OUTPUT_MM_MULTI: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of multi loop mismatch contribution

VRNA_CONVERT_OUTPUT_MM_EXT: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of exterior loop mismatch contribution

VRNA_CONVERT_OUTPUT_DANGLE5: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 5’ dangle conctribution

VRNA_CONVERT_OUTPUT_DANGLE3: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 3’ dangle contribution

VRNA_CONVERT_OUTPUT_INT_11: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 1:1 interior loop contribution

VRNA_CONVERT_OUTPUT_INT_21: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 2:1 interior loop contribution

VRNA_CONVERT_OUTPUT_INT_22: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of 2:2 interior loop contribution

VRNA_CONVERT_OUTPUT_BULGE: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of bulge loop contribution

VRNA_CONVERT_OUTPUT_INT: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of interior loop contribution

VRNA_CONVERT_OUTPUT_ML: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of multi loop contribution

VRNA_CONVERT_OUTPUT_MISC: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of misc contributions (such as terminalAU)

VRNA_CONVERT_OUTPUT_SPECIAL_HP: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of special hairpin contributions (tri-, tetra-, hexa-loops)

VRNA_CONVERT_OUTPUT_VANILLA: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of given parameters only

Note

This option overrides all other output options, except VRNA_CONVERT_OUTPUT_DUMP !

VRNA_CONVERT_OUTPUT_NINIO: #include <ViennaRNA/params/convert.h>
Flag to indicate printing of interior loop asymmetry contribution

VRNA_CONVERT_OUTPUT_DUMP: #include <ViennaRNA/params/convert.h>
Flag to indicate dumping the energy contributions from the library instead of an input file

Functions

void convert_parameter_file(const char *iname, const char *oname, unsigned int options)

#include <ViennaRNA/params/convert.h>

Convert/dump a Vienna 1.8.4 formatted energy parameter file

The options argument allows one to control the different output modes.

Currently available options are:

The defined options are fine for bitwise compare- and assignment-operations, e. g.: pass a collection of options as a single value like this:

convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n)

Parameters

iname – The input file name (If NULL input is read from stdin)
oname – The output file name (If NULL output is written to stdout)
options – The options (as described above)